|Jennifer Ivey Middlebrooks|
|Thursday, 01 October 2009 00:00|
Bioinformatics is a powerful tool for deducing protein function through transitivity and process of elimination. Here we present the case of the LUng Seven Transmembrane Receptor (LUSTR) protein family as an example of bioinformatics as a deductive tool. Currently, LUSTRs are annotated as G-protein-coupled receptors (GPCR).
LUSTRs were categorized as GPCRs in a cursory study by Edgar because they possess several of the identifying GPCR characteristics including seven transmembrane spanning regions, an extracellular amino terminus of variable sequence used for ligand binding, an intracellular carboxyl terminus, and a third intracellular loop that is highly conserved and predicted to bind heterotrimeric GTPases, consisting of an α, a β, and a γ subunit, called Gproteins. (Edgar, 2002 and Edgar, 2007). The LUSTR family includes two subfamilies. Subfamily A (LUSTR-A) (historically referred to as GPR107 and GPR108) has been found exclusively in plants and animals, while subfamily B (LUSTR-B) (historically referred to as TMEM87A and TMEM87B) has also been indentified in multiple fungal classes.
Recently, a LUSTR-A homolog was found in the algal species Chlamydomonas reinhardttii. Chlamydomonas are unicellular, biflagellate organisms with characteristics of both plants and animals (Wheeler and Brownlee, 2008; Merchant et al., 2007), and have been the predominate model for studying flagella (also known as cilia). These organisms are unique in their ability to excise their flagella under environmental stress and fully regenerate them within two hours. The signal transduction mechanisms and gene expression regulation related to this event have been studied for decades but still remain undefined. An array experiment focusing on the gene expression response of flagellar regeneration after environmental stress found a greater than two fold increase in a LUSTR-A homolog (Cr7TM), referred to in the study as a G-protein coupled seven transmembrane protein (Chamberlain et al., 2008).
Hypothesized to be the GPCR responsible for flagellar excision, Cr7TM became the focus of our bioinformatic search. Expecting to uncover the type of ligand that interacts with the extracellular N-terminus and the type of G-protein subunits that bind to the third intracellular loop of the receptor, I instead discovered that LUSTRs show no significant similarity to known GPCR sequences, motifs, or domains, and expanded my search to determine the true function of LUSTR proteins.